RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 043141
(135 letters)
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation;
2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X
2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y
Length = 365
Score = 97.3 bits (243), Expect = 3e-25
Identities = 25/55 (45%), Positives = 35/55 (63%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLR 85
E +D ++SGPGGQ +N +SAVR+ H+PTG+ RSQ KN+ AL L+
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILK 280
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 90.9 bits (226), Expect = 5e-25
Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 21 LELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA 80
L L + EL E K GPGGQ NK + V +KHVP+G++ + + RS +NR A
Sbjct: 41 LPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIA 96
Query: 81 LSRLRTLL 88
L+ +
Sbjct: 97 RKVLQEKV 104
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular
mimicry, translation; 1.81A {Escherichia coli} SCOP:
e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Length = 365
Score = 96.2 bits (240), Expect = 8e-25
Identities = 29/58 (50%), Positives = 43/58 (74%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
+ +D Y++SG GGQH+N+ ESAVRI H+PTG++ Q DRSQHKN+ A+ +++ L
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKL 295
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor
1 (RF-1), structural joint center for structural
genomics, JCSG; 2.34A {Streptococcus mutans}
Length = 371
Score = 94.6 bits (236), Expect = 2e-24
Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
+ +D Y +SG GGQ++NK +AVRI H+PT + + E+R+Q KNR A+ +R +
Sbjct: 234 DLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARV 291
>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein,
ribosomal protein, RNA-binding, binding, metal-binding,
zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y
3d5c_X 3mr8_V 3ms0_V
Length = 354
Score = 94.2 bits (235), Expect = 3e-24
Identities = 28/58 (48%), Positives = 39/58 (67%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
E +D ++SGPGGQ +N +SAVR+ H+PTG++ + RSQ KNR AL LR+ L
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRL 273
>2b3t_B RF-1, peptide chain release factor 1; translation termination,
methylation, conformational changes; HET: SAH; 3.10A
{Escherichia coli} SCOP: e.38.1.1
Length = 360
Score = 93.8 bits (234), Expect = 4e-24
Identities = 28/58 (48%), Positives = 43/58 (74%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
+ +DT++SSG GGQH+N +SA+RI H+PTG++ + ++RSQHKN+ ALS L +
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARI 278
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide
release factor 1, ribosome, structural genomics, BSGC
structure funded by NIH; 2.65A {Thermotoga maritima}
SCOP: e.38.1.1 PDB: 2fvo_A
Length = 342
Score = 92.7 bits (231), Expect = 1e-23
Identities = 27/55 (49%), Positives = 42/55 (76%)
Query: 34 MDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
++T+++SG GGQ++NK ESAVRI H+PTG++ +RSQ++N+ +AL LR L
Sbjct: 200 IETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARL 254
>4dh9_Y YAEJ; ribosome, YAEJ, ribosome stalling, ribosome rescue, rescue
F alternative rescue factor, ARFB, release factor,
rescue of ribosomes; 3.20A {Escherichia coli} PDB:
2jy9_A
Length = 140
Score = 64.0 bits (156), Expect = 2e-14
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 24/83 (28%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIK------------------------HVPTGVIAQ 66
E E+ ++ G GGQH+NK +A+ ++ ++ +
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIK 73
Query: 67 AAEDRSQHKNRVSALSRLRTLLA 89
A E RSQ NR +AL+RL ++
Sbjct: 74 AQEYRSQELNREAALARLVAMIK 96
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 62.6 bits (152), Expect = 5e-14
Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 24/83 (28%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTG------------------------VIAQ 66
E E+ ++ G GGQ++NK SA+ ++ ++ +
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLK 73
Query: 67 AAEDRSQHKNRVSALSRLRTLLA 89
A + R+Q +NR AL RL L+
Sbjct: 74 AQQYRTQEQNRADALLRLSELIV 96
>1j26_A Immature colon carcinoma transcript 1; peptide chain release
factors, RF-1, the GGQ motif, immature carcinoma
transcript 1; NMR {Mus musculus} SCOP: d.50.4.1
Length = 112
Score = 54.4 bits (130), Expect = 7e-11
Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 25/84 (29%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTG-------------------------VIA 65
+ +SSGPGGQ++NK S ++ ++
Sbjct: 21 RLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVL 80
Query: 66 QAAEDRSQHKNRVSALSRLRTLLA 89
+ R Q +N L ++R ++A
Sbjct: 81 TSESSRYQFRNLAECLQKIRDMIA 104
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 31.9 bits (72), Expect = 0.054
Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 17/95 (17%)
Query: 36 TYKSSG--PGGQHINKRESAVRIKHVPTGV-IAQAAEDRSQHKNRVSALSRLRTLLALNV 92
T K G PG + + + + T V IA+ S + A + L + V
Sbjct: 252 TAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKA---ITVLFFIGV 308
Query: 93 RSSVKLDAY---SPPPQLLQILPPKSTIRSSEVGP 124
R +AY S PP +L+ ++ ++E P
Sbjct: 309 RC---YEAYPNTSLPPSILE-----DSLENNEGVP 335
>3cny_A Inositol catabolism protein IOLE; xylose isomerase-like TIM barrel,
structural genomics, joint for structural genomics,
JCSG; 1.85A {Lactobacillus plantarum WCFS1}
Length = 301
Score = 30.0 bits (67), Expect = 0.21
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 2/60 (3%)
Query: 1 MCYHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINK-RESAVRIKHV 59
+ YH + + + TD +L DT + G ++ R+ HV
Sbjct: 157 VAYHHHMGTGIQTKEETDRLMANTDPKLVG-LLYDTGHIAVSDGDYMALLNAHIDRVVHV 215
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 28.7 bits (63), Expect = 0.64
Identities = 16/121 (13%), Positives = 32/121 (26%), Gaps = 39/121 (32%)
Query: 15 SSKKNYLELTDDE---LFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDR 71
S + + LT DE L + +D P + P ++ AE
Sbjct: 290 SLDHHSMTLTPDEVKSLLLKY-LDCRPQDLP--------REVLTTN--PR-RLSIIAESI 337
Query: 72 SQHKNRVSALSRLRTLLALNVRSSVK--LDAYSP-------------------PPQLLQI 110
+ + + + ++ L+ P P LL +
Sbjct: 338 RDGLAT---WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394
Query: 111 L 111
+
Sbjct: 395 I 395
Score = 26.7 bits (58), Expect = 3.4
Identities = 25/131 (19%), Positives = 43/131 (32%), Gaps = 27/131 (20%)
Query: 1 MCYHTNDNCSSSSSSSKKNYLELTD--DELFRECEMDTYKSS--------GPGGQHINKR 50
+ Y + N +S S S L + EL R + Y++ + N
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNA--KAWNAF 262
Query: 51 ESAVRI------KHVPTGVIAQAAEDRSQ-HKNRVSALSRLRTLLA--LNVRSSVKLDAY 101
+ +I K V + A S H + +++LL L+ R L
Sbjct: 263 NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ-DL--- 318
Query: 102 SPPPQLLQILP 112
P ++L P
Sbjct: 319 --PREVLTTNP 327
>3mal_A Stromal cell-derived factor 2-like protein; trefoil fold, MIR
motifs, unfolded protein response, putativ binding
protein, plant protein; 1.95A {Arabidopsis thaliana}
Length = 199
Score = 27.2 bits (60), Expect = 1.7
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 43 GGQHINKRESAVRIKHVPTGV 63
G K++ VR++H+ T
Sbjct: 133 GSGKTWKQDQRVRLQHIDTSG 153
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.1 bits (56), Expect = 3.3
Identities = 4/23 (17%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 45 QHINKRESAVRIKHVPTGVIAQA 67
Q + K ++++++ + A A
Sbjct: 20 QALKKLQASLKL-YADDSAPALA 41
Score = 25.7 bits (55), Expect = 4.1
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 12/38 (31%)
Query: 80 ALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTI 117
AL +L+ +S+KL A P L I K+T+
Sbjct: 21 ALKKLQ--------ASLKLYADDSAPA-LAI---KATM 46
>1t9f_A Protein 1D10; structural genomics, PSI, protein structure
initiative, southeast collaboratory for structural
genomics, secsg; 2.00A {Caenorhabditis elegans} SCOP:
b.42.6.1
Length = 187
Score = 26.1 bits (57), Expect = 3.8
Identities = 3/15 (20%), Positives = 6/15 (40%)
Query: 49 KRESAVRIKHVPTGV 63
+++H TG
Sbjct: 127 LESEQFKLRHAVTGS 141
>2xoa_A Ryanodine receptor 1; metal transport, calcium channel, ION
channel, membrane PROT malignant hyperthermia, cardiac
arrhythmia; 2.50A {Oryctolagus cuniculus}
Length = 559
Score = 25.6 bits (55), Expect = 6.8
Identities = 8/35 (22%), Positives = 13/35 (37%)
Query: 29 FRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGV 63
+ G G I ES ++HV +G+
Sbjct: 321 EKLDTAPKRDVEGMGPPEIKYGESLCFVQHVASGL 355
>3p01_A Two-component response regulator; PSI-2, midwest center for
structural genomics, protein struc initiative, MCSG,
signali protein; 2.65A {Nostoc SP}
Length = 184
Score = 25.3 bits (56), Expect = 6.9
Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 12/55 (21%)
Query: 63 VIAQAAEDRSQHKNRVSALSR----LRTLLALN--VRSSVKLDAYSPPPQLLQIL 111
V+ +AAE K R L R + L L ++S +L +
Sbjct: 4 VVQRAAETYDLLKQRTEELRRANAQMSLLTVLVQVTQAS--NS----LEAILTPI 52
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.312 0.127 0.361
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,850,131
Number of extensions: 94555
Number of successful extensions: 111
Number of sequences better than 10.0: 1
Number of HSP's gapped: 108
Number of HSP's successfully gapped: 22
Length of query: 135
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 51
Effective length of database: 4,356,429
Effective search space: 222177879
Effective search space used: 222177879
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.0 bits)